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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgccatttcagtacttatttgtcttgtggaatgtgttccattttatgccactgttctcgaaatgtgattgcttgcgcattttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG

Basic information

species Zea mays
transcript GRMZM2G062210_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062210_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g02540.1 (Oryza sativa), 3'ss of exon 3
gtttgccatttcagtacttatttgtcttgtggaatgtgttccattttatgccactgttctcgaaatgtgattgcttgcgcattttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG
||||||  | |     |||||||    | |||  ||||||||  ||||  ||| ||| ||| | || ||||||  |   ||||||  | |||||||||| || ||||| |  || ||||| |||||||||||||||||||||||||| ||||| || ||||||||||| ||| ||||
gtttgctttctgttcgcttatttcctgtctggg-tgtgttcc--tttaaaccattgtactc-agatatgattgaataaacattttttacagAGCAAAGTTATCGACAACAGTAATTTCCGAAACTTTCTGGAGCTGGTGCCTGAAGTGAGGGAACTTGTTAATGATTTCTATTCAAG

upper sequence: GRMZM2G062210_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttgccatttcagtacttatttgtcttgtggaatgtgttccattttatgccactgttctcgaaatgtgattgcttgcgcattttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG
    ||   |    || |||    |  | |  | | ||  |||||||   |||     || |   | | | |   | |  ||||||||  |   |||||||||||||||||||||||||| || ||  ||||||| |||||||| || ||||| ||  | || ||||| ||| ||||
----gcatgtatcctatttagcatttcttttaactctg--ccatttttctcca--acacttggtctataacttagt-ctaattttgca--gCAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAG

upper sequence: GRMZM2G062210_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------------------gtttgccatttcagtacttat--ttgtcttgtggaatgtgttccattttatgccactgttctcgaaatgtgattgcttgcgcattttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG
                                                          | ||| ||   ||   ||||  |    | ||   |||  ||  |||   |   |   |   | |  |||      |||           ||||| ||||| |||||||| ||||||||||| || ||| ||||||| || ||||||||  | |||||| |  |||| |||||||| ||
gtaaaataccaaaccctcttttaattattttttttagtgatctttctggcttataaactctgctatcgtagcttttatcatgagttagtaagatggatttaattcattttaatcatgtccaatctgtcgccaattg----------gtagAGTAAAGTGATTGACAACATCAACTTCCGCAATTTTTTGGAGCTTGTCCCTGAAGTGCGAGAGCTGATCCATGACTTTTATGCGAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60401615|gb|DN234422.1|DN234422
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAG                         AGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
EST: gi|32797927|gb|CD950163.1|CD950163
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAG                         AGCAAAGTCATTGGCAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
EST: gi|211125416|gb|FL031454.1|FL031454
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAG                         AGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
EST: gi|22819870|gb|BU499960.1|BU499960
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAG                         AGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
EST: gi|60345822|gb|DN212795.1|DN212795
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAG                         AGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
EST: gi|60401180|gb|DN233987.1|DN233987
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAG                         AGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
EST: gi|20811311|gb|BQ295789.1|BQ295789
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCATACCTGAAG                         AGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
EST: gi|5847125|gb|AW000204.1|AW000204
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAG                         AGCAAAG-CATTGACAATA
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATA
EST: gi|18660332|gb|BM500807.1|BM500807
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAG                         AGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
EST: gi|211125417|gb|FL031455.1|FL031455
EST:     TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAG                         AGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT
genomic: TCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 228

TGAACTAGGAAACAACTTCTCTGAAGTCATAGCTCCTCAAGACGTGGCAGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

TGAACTAGGAAACAACTTCTCTGAAGTCATAGCTCCTCAAGACGTGGCAGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 212

TGAACTAGGAAACAACTTCTCTGAAGTCATAGCTCCTCAAGACGTGGCAGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

TGAACTAGGAAACAACTTCTCTGAAGTCATAGCTCCTCAAGACGTGGCAGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTTGACCGTTCAGACCTGAAGgtttgccatt ... ttttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttccattttatgccactgttctcgaaatgtgattgcttgcgcattttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG
      attttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgccatttcagtacttatttgtcttgtggaatgtgttccattttatgccactgttctcgaaatgtgattgcttgcgcattttgcatagAGCAAAGTCATTGACAATATCAACTTCCGTAACTTTCTGGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTTATGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT